Mercurial > repos > immport-devteam > profile_cl
comparison profileCLs.xml @ 1:62d8985a41e2 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
| author | azomics |
|---|---|
| date | Thu, 23 Jul 2020 08:58:29 -0400 |
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| 0:8547aedf1350 | 1:62d8985a41e2 |
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| 1 <tool id="get_profiles_cell_ontology" name="Associate FLOCK populations" version="1.1+galaxy0" profile="18.01"> | |
| 2 <description>with cell ontology</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.11.2">jinja2</requirement> | |
| 5 <requirement type="package" version="1.26.0">bioconductor-flowcl</requirement> | |
| 6 </requirements> | |
| 7 <stdio> | |
| 8 <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." /> | |
| 9 <exit_code range="3:" level="fatal" description="See stderr for more details." /> | |
| 10 </stdio> | |
| 11 <command><![CDATA[ | |
| 12 python '$__tool_directory__/profileCLs.py' -i '${input}' -o '${html_file}' -d '${html_file.files_path}' -t '$__tool_directory__' | |
| 13 ]]> | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param format="flowscore" name="input" type="data" label="Population score profiles from FLOCK"/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="html" name="html_file" label="Cell ontology of ${input.name}"> | |
| 20 </data> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="input" value="input.flowscore"/> | |
| 25 <output name="html_file" file="out.html"> | |
| 26 <extra_files type="file" name="CLprofiles.txt" value="CLprofiles.txt"/> | |
| 27 <extra_files type="file" name="flowcl_pop01.pdf" value="flowcl_pop01.pdf" compare="sim_size"/> | |
| 28 <extra_files type="file" name="flowcl_pop01.txt" value="flowcl_pop01.txt"/> | |
| 29 <extra_files type="file" name="flowcl_pop03.pdf" value="flowcl_pop03.pdf" compare="sim_size"/> | |
| 30 <extra_files type="file" name="flowcl_pop03.txt" value="flowcl_pop03.txt"/> | |
| 31 <extra_files type="file" name="scores.txt" value="scores.txt"/> | |
| 32 </output> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help><![CDATA[ | |
| 36 This tool uses flowCL to find a match for each of the populations defined by FLOCK. | |
| 37 .. class:: warningmark | |
| 38 Please note that the scores computed for each markers and population correspond to quartiles binning, and not necessarily to what would be considered +, -, low or high. | |
| 39 ----- | |
| 40 **Input** | |
| 41 This tool reads in the population score profiles from FLOCK. | |
| 42 .. class:: warningmark | |
| 43 **The marker names need to be in the cell ontology for this to work** | |
| 44 **Output** | |
| 45 The output is a page that allows visualization of the data. | |
| 46 ----- | |
| 47 **Example** | |
| 48 *Input* | |
| 49 *Population profile file*:: | |
| 50 Population_ID Marker1 Marker2 Marker3 ... Count Percentage | |
| 51 1 1 3 2 ... 3885 6.44 | |
| 52 2 1 3 4 ... 2774 4.62 | |
| 53 3 2 2 3 ... 2151 3.59 | |
| 54 4 1 3 2 ... 1207 2.01 | |
| 55 ... ... ... ... ... ... ... | |
| 56 *Output* | |
| 57 The CL terms hyperlink to their representation in the Immport Cell Ontology browser. The full flowCL run summary is accessible by clicking on the phenotype. | |
| 58 .. image:: ../../static/images/flowtools/profileCL.png | |
| 59 .. image:: ../../static/images/flowtools/popprofiles.png | |
| 60 ]]> | |
| 61 </help> | |
| 62 <citations> | |
| 63 <citation type="doi">10.1093/bioinformatics/btu807</citation> | |
| 64 </citations> | |
| 65 </tool> |